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Ferreira PFA, Rocha FI, Howe A, Barbosa DR, da Conceição Jesus E, do Amaral Sobrinho NMB, da Silva Coelho I. Chemical attributes, bacterial community, and antibiotic resistance genes are affected by intensive use of soil in agro-ecosystems of the Atlantic Forest, Southeastern Brazil. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:123. [PMID: 38483669 DOI: 10.1007/s10653-024-01894-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/29/2024] [Indexed: 03/19/2024]
Abstract
Soil is one of the largest reservoirs of microbial diversity in nature. Although soil management is vital for agricultural purposes, intensive practices can have a significant impact on fertility, microbial community, and resistome. Thus, the aim of this study was to evaluate the effects of an intensive soil management system on the chemical attributes, composition and structure of prevalent bacterial communities, and presence and abundance of antimicrobial resistance genes (ARGs). The chemical characterization, bacterial diversity and relative abundance of ARGs were evaluated in soils from areas of intensive vegetable cultivation and forests. Results indicate that levels of nutrients and heavy metals were higher in soil samples from cultivated areas. Similarly, greater enrichment and diversity of bacterial genera was detected in agricultural areas. Of the 18 target ARGs evaluated, seven were detected in studied soils. The oprD gene exhibited the highest abundance among the studied genes and was the only one that showed a significantly different prevalence between areas. The oprD gene was identified only from soil of the cultivated areas. The blaSFO, erm(36), oprD and van genes, in addition to the pH, showed greater correlation with in soil of cultivated areas, which in turn exhibited higher contents of nutrients. Thus, in addition to changes in chemical attributes and in the microbial community of the soil, intensive agricultural cultivation systems cause a modification of its resistome, reinforcing the importance of the study of antimicrobial resistance in a One Health approach.
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Affiliation(s)
- Paula Fernanda Alves Ferreira
- Departament of Soil, Institute of Agronomy, Federal Rural University of Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-970, Brazil
| | - Fernando Igne Rocha
- Mokichi Okada Research Center, Korin Agriculture and Environment, Ipeúna, São Paulo, Brazil
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
| | - Daniele Rodrigues Barbosa
- Departament of Soil, Institute of Agronomy, Federal Rural University of Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-970, Brazil
| | - Ederson da Conceição Jesus
- Embrapa Agrobiology, Brazilian Agricultural Research Corporation, Seropédica, Rio de Janeiro, 23891-000, Brazil
| | | | - Irene da Silva Coelho
- Department of Veterinary Microbiology and Immunology, Veterinary Institute, Federal Rural University of Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-970, Brazil.
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2
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Rocha FI, Jesus EDC, Teixeira WG, Lumbreras JF, Clemente EDP, da Motta PEF, Borsanelli AC, Dutra IDS, de Oliveira AP. Soil type determines the magnitude of soil fertility changes by forest-to-pasture conversion in Western Amazonia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:158955. [PMID: 36155034 DOI: 10.1016/j.scitotenv.2022.158955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/18/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
The deforestation of tropical forests raises environmental concerns worldwide. Removing the pristine forest impacts the soil, consequently affecting the environmental services it provides. Within this context, the main goal of this study was to determine how the conversion of the tropical rainforest to pasture affects soil fertility across an extended range of soil heterogeneity, including different soil types. We sampled 13 sites, among forests, recent pastures (≤7-year-old), and old pastures (≥10-year-old), on Acrisols, Ferralsols, Plinthosols, and Luvisols, across a ± 800 km geographical range in the Western Brazilian Amazon. Soils were classified taxonomically, and their superficial layer's chemical and physical properties (0-10 cm) were analyzed. Furthermore, we tested the sensibility of Actinobacteria and Proteobacteria to detect changes in these soil properties based on their ecological habitat. An inter-regional gradient of soil fertility was observed, and the sampling sites were clustered mostly by soil type and associated land use than by spatial distance. The Sum of bases, Ca + Mg, base saturation, Al saturation, and pH were consistently affected by land use, increasing after conversion to pasture, at different degrees and with a more pronounced effect on oxidic soils. The Sum of bases was the only property that increased significantly among the study sites (Radj = 0.860, p < 0.001), being able to detect the effect of anthropic land use on a larger coverage of soil types. Finally, the Actinobacteria:Proteobacteria ratio was also sensitive to the impact of forest-to-pasture conversion, with a higher ratio observed in pasture systems, and it was positively correlated with soil pH (rho = 0.469, p < 0.001). Our results consistently show that the forest-to-pasture conversion leads to strong alterations in the soil environment, with varying intensities depending on soil type.
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Affiliation(s)
- Fernando Igne Rocha
- Department of Soil Science, Federal Rural University of Rio de Janeiro (UFRRJ), Seropédica, RJ, Brazil; National Agrobiology Research Center, Embrapa Agrobiologia, Seropédica, RJ, Brazil.
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3
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Gutierrez A, Grillo MA. Effects of Domestication on Plant-Microbiome Interactions. PLANT & CELL PHYSIOLOGY 2022; 63:1654-1666. [PMID: 35876043 DOI: 10.1093/pcp/pcac108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 07/15/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Through the process of domestication, selection is targeted on a limited number of plant traits that are typically associated with yield. As an unintended consequence, domesticated plants often perform poorly compared to their wild progenitors for a multitude of traits that were not under selection during domestication, including abiotic and biotic stress tolerance. Over the past decade, advances in sequencing technology have allowed for the rigorous characterization of host-associated microbial communities, termed the microbiome. It is now clear that nearly every conceivable plant interaction with the environment is mediated by interactions with the microbiome. For this reason, plant-microbiome interactions are an area of great promise for plant breeding and crop improvement. Here, we review the literature to assess the potential impact that domestication has had on plant-microbiome interactions and the current understanding of the genetic basis of microbiome variation to inform plant breeding efforts. Overall, we find limited evidence that domestication impacts the diversity of microbiomes, but domestication is often associated with shifts in the abundance and composition of microbial communities, including taxa of known functional significance. Moreover, genome-wide association studies and mutant analysis have not revealed a consistent set of core candidate genes or genetic pathways that confer variation in microbiomes across systems. However, such studies do implicate a consistent role for plant immunity, root traits, root and leaf exudates and cell wall integrity as key traits that control microbiome colonization and assembly. Therefore, selection on these key traits may pose the most immediate promise for enhancing plant-microbiome interactions through breeding.
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Affiliation(s)
- Andres Gutierrez
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
| | - Michael A Grillo
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
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Ma S, Zhu B, Chen G, Ni X, Zhou L, Su H, Cai Q, Chen X, Zhu J, Ji C, Li Y, Fang J. Loss of soil microbial residue carbon by converting a tropical forest to tea plantation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151742. [PMID: 34808187 DOI: 10.1016/j.scitotenv.2021.151742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 11/05/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
Land-use change can lead to profound changes in the storage of soil organic carbon (SOC) in the tropics. Soil microbial residues make up the majority of persistent SOC pools, yet the impact of land-use change on microbial residue C accumulation in the tropics is not well understood. Here, we investigated how the conversion of tropical primary montane rainforest to secondary forest and the conversions of secondary forest to Prunus salicina plantation and tea plantation, influence the accumulation of soil microbial residue C (indicated by amino sugars). Our results showed that the secondary forest had a higher SOC than that of the primary forest (+63%), while they had no difference in microbial residue C concentration, indicating a relatively slow microbial-derived C accrual during secondary succession. Moreover, the P. salicina plantation and tea plantation had lower SOC than the secondary forest (-53% and -57%, respectively). A decrease in fungal biomass (-51%) resulted in less fungal and total residue C concentrations in the tea plantation than in the secondary forest (-38% and -35%, respectively), indicating microbial-derived C loss following the forest conversion. The change in microbial residue C depended on litter standing crop rather than soil nutrient and root biomass. Litter standing crop affected microbial residue C concentration by regulating fungal biomass and hydrolytic enzyme activities. Taken together, our results highlight that litter-microbe interactions drive microbial residue C accumulation following forest conversions in the tropics.
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Affiliation(s)
- Suhui Ma
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Biao Zhu
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China.
| | - Guoping Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Xiaofeng Ni
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Luhong Zhou
- School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Haojie Su
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Qiong Cai
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Xiao Chen
- State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry (LAPC), Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, China
| | - Jiangling Zhu
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Chengjun Ji
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Yide Li
- Jianfengling National Key Field Observation and Research Station for Forest Ecosystem, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China
| | - Jingyun Fang
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
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Hulsmans E, Peeters G, Honnay O. Soil Microbiomes in Apple Orchards Are Influenced by the Type of Agricultural Management but Never Match the Complexity and Connectivity of a Semi-natural Benchmark. Front Microbiol 2022; 13:830668. [PMID: 35250946 PMCID: PMC8888915 DOI: 10.3389/fmicb.2022.830668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/20/2022] [Indexed: 11/22/2022] Open
Abstract
Conversion of natural ecosystems into agricultural land may strongly affect the soil microbiome and the functioning of the soil ecosystem. Alternative farming systems, such as organic farming, have therefore been advocated to reduce this impact, yet the outcomes of different agricultural management regimes often remain ambiguous and their evaluations mostly lack a proper more natural benchmark. We used high-throughput amplicon sequencing, linear models, redundancy analyses, and co-occurrence network analyses to investigate the effect of organic and integrated pest management (IPM) on soil fungal and bacterial communities in both the crop and drive rows of apple orchards in Belgium, and we included semi-natural grasslands as a benchmark. Fungi were strongly influenced by agricultural management, with lower diversity indices and distinct communities in IPM compared to organic orchards, whereas IPM orchards had a higher AMF abundance and the most complex and connected fungal communities. Bacterial diversity indices, community composition, and functional groups were less affected by management, with only a higher network connectivity and abundance of keystone taxa in organic drive rows. On the other hand, none of the agricultural soil microbiomes matched the complexity and connectedness of our semi-natural benchmark, demonstrating that even more nature-friendly agricultural management practices strongly affect the soil microbiome and highlighting the essential role of (semi-)natural systems as a harbor of robust and functionally diverse fungal and bacterial communities.
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Affiliation(s)
- Eva Hulsmans
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Leuven, Belgium
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6
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Becerra-Lucio AA, Labrín-Sotomayor NY, Becerra-Lucio PA, Trujillo-Elisea FI, Chávez-Bárcenas AT, Machkour-M'Rabet S, Peña-Ramírez YJ. Diversity and Interactomics of Bacterial Communities Associated with Dominant Trees During Tropical Forest Recovery. Curr Microbiol 2021; 78:3417-3429. [PMID: 34244846 DOI: 10.1007/s00284-021-02603-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 07/01/2021] [Indexed: 10/20/2022]
Abstract
Bacterial communities have been identified as functional key members in soil ecology. A deep relation with these communities maintains forest coverture. Trees harbor particular bacteriomes in the rhizosphere, endosphere, or phyllosphere, different from bulk-soil representatives. Moreover, the plant microbiome appears to be specific for the plant-hosting species, varies through season, and responsive to several environmental factors. This work reports the changes in bacterial communities associated with dominant pioneer trees [Tabebuia rosea and Handroanthus chrysanthus [(Bignoniaceae)] during tropical forest recovery chronosequence in the Mayan forest in Campeche, Mexico. Massive 16S sequencing approach leads to identifying phylotypes associated with rhizosphere, bulk-soil, or recovery stage. Lotka-Volterra interactome modeling suggests the presence of putative regulatory roles of some phylotypes over the rest of the community. Our results may indicate that bacterial communities associated with pioneer trees may establish more complex regulatory networks than those found in bulk-soil. Moreover, modeled regulatory networks predicted from rhizosphere samples resulted in a higher number of nodes and interactions than those found in the analysis of bulk-soil samples.
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Affiliation(s)
- Angel A Becerra-Lucio
- Department of Sustainability Sciences, El Colegio de la Frontera Sur Unidad Campeche, Av. Rancho Polígono 2-A Col. Ciudad Industrial, Lerma, CP 24500, Campeche, Campeche, México
| | - Natalia Y Labrín-Sotomayor
- Department of Sustainability Sciences, El Colegio de la Frontera Sur Unidad Campeche, Av. Rancho Polígono 2-A Col. Ciudad Industrial, Lerma, CP 24500, Campeche, Campeche, México
| | - Patricia A Becerra-Lucio
- Department of Sustainability Sciences, El Colegio de la Frontera Sur Unidad Campeche, Av. Rancho Polígono 2-A Col. Ciudad Industrial, Lerma, CP 24500, Campeche, Campeche, México
| | - Flor I Trujillo-Elisea
- Department of Sustainability Sciences, El Colegio de la Frontera Sur Unidad Campeche, Av. Rancho Polígono 2-A Col. Ciudad Industrial, Lerma, CP 24500, Campeche, Campeche, México
| | - Ana T Chávez-Bárcenas
- Agrobiologia School, Universidad Michoacana de San Nicolás de Hidalgo, CP 6017, Uruapan, Michoacán, México
| | - Salima Machkour-M'Rabet
- Department of Biodiversity Conservation, El Colegio de la Frontera Sur Unidad Chetumal, Av. Centenario km 5.5, CP 77014, Chetumal, Quintana Roo, México
| | - Yuri J Peña-Ramírez
- Department of Sustainability Sciences, El Colegio de la Frontera Sur Unidad Campeche, Av. Rancho Polígono 2-A Col. Ciudad Industrial, Lerma, CP 24500, Campeche, Campeche, México.
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7
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Rocha FI, Ribeiro TG, Fontes MA, Schwab S, Coelho MRR, Lumbreras JF, da Motta PEF, Teixeira WG, Cole J, Borsanelli AC, Dutra IDS, Howe A, de Oliveira AP, Jesus EDC. Land-Use System and Forest Floor Explain Prokaryotic Metacommunity Structuring and Spatial Turnover in Amazonian Forest-to-Pasture Conversion Areas. Front Microbiol 2021; 12:657508. [PMID: 33967996 PMCID: PMC8097146 DOI: 10.3389/fmicb.2021.657508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/29/2021] [Indexed: 01/04/2023] Open
Abstract
Advancing extensive cattle production is a major threat to biodiversity conservation in Amazonia. The dominant vegetation cover has a drastic impact on soil microbial communities, affecting their composition, structure, and ecological services. Herein, we explored relationships between land-use, soil types, and forest floor compartments on the prokaryotic metacommunity structuring in Western Amazonia. Soil samples were taken in sites under high anthropogenic pressure and distributed along a ±800 km gradient. Additionally, the litter and a root layer, characteristic of the forest environment, were sampled. DNA was extracted, and metacommunity composition and structure were assessed through 16S rRNA gene sequencing. Prokaryotic metacommunities in the bulk soil were strongly affected by pH, base and aluminum saturation, Ca + Mg concentration, the sum of bases, and silt percentage, due to land-use management and natural differences among the soil types. Higher alpha, beta, and gamma diversities were observed in sites with higher soil pH and fertility, such as pasture soils or fertile soils of the state of Acre. When taking litter and root layer communities into account, the beta diversity was significantly higher in the forest floor than in pasture bulk soil for all study regions. Our results show that the forest floor's prokaryotic metacommunity performs a spatial turnover hitherto underestimated to the regional scale of diversity.
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Affiliation(s)
- Fernando Igne Rocha
- Department of Soil, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | | | | | - Stefan Schwab
- National Agrobiology Research Center, Embrapa Agrobiologia, Seropédica, Brazil
| | | | | | | | | | - James Cole
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | | | - Iveraldo dos Santos Dutra
- Department of Support, Production and Animal Health, Universidade Estadual Paulista, Araçatuba, Brazil
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
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Díaz‐Vallejo EJ, Seeley M, Smith AP, Marín‐Spiotta E. A meta‐analysis of tropical land‐use change effects on the soil microbiome: Emerging patterns and knowledge gaps. Biotropica 2021. [DOI: 10.1111/btp.12931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Megan Seeley
- School of Geographical Studies and Urban Planning Arizona State University Tempe AZ USA
| | - A. Peyton Smith
- Department of Crops and Soil Science Texas A&M University Agriculture and Life Sciences College Station TX USA
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9
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Abbasi F, Jalili M, Samaei MR, Mokhtari AM, Azizi E. Effect of land use on cultivable bioaerosols in the indoor air of hospital in southeast Iran and its determination of the affected radius around of hospital. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:12707-12713. [PMID: 33094460 DOI: 10.1007/s11356-020-10357-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
This study aimed to evaluate the effect of land use on hospital bioaerosols and determine the effective radius. The concentration of fungi and bacteria in indoor and outdoor air was determined by the 0800NIOSH. Then land uses were determined by Google earth within a range of 0.5-5 km around three hospitals. Data were analyzed by using Spearman correlation, and a t test was used to determine differences between groups. Data were recorded in Excel and entered into Matlab2018 for analysis. The results of the study showed that the concentration of fungi and bacteria was higher in the indoor and outdoor hospital B (bacteria = 343-43, fungi = 106-291 CFU/m3) (P = 0.04). Maximum land use was also found in hospitals A and B related to urban and bare, while in hospital C, they were urban and bare. Mathematical modeling has shown that the trend of land-use variation over different radii consisted of the Gaussian model (in hospital B) and Fourier series (in hospitals A and C). Besides, there was a positive correlation between the bare and fungal and bacterial concentrations. Finally, the most effective bare radius of application on the indoor and outdoor fungi was 4 and 5 km, respectively (R2 = 0.99). The effective radius for reducing fungi and bacteria by creating green space was 0.5 and 3 km from the hospital center (R2fungi = - 0.99, R2bacteria = - 0.8). Based on these results, land use is an effective factor in airborne fungi and bacteria in hospitals. Therefore, their control and management of land use during 5 km is necessary to reduce pollution.
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Affiliation(s)
- Fariba Abbasi
- Department of Environmental Health Engineering, Shiraz University of Medical Science, Shiraz, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahrokh Jalili
- Environmental Science and Technology Research Center, Department of Environmental Health Engineering, School of Public Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Student Research Committee, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohammad Reza Samaei
- Research Center for Health Sciences, Institute of Health, Department of Environmental Health, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
| | | | - Elahe Azizi
- Department of Environmental Health Engineering, Shiraz University of Medical Science, Shiraz, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
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Novoa A, Keet JH, Lechuga-Lago Y, Pyšek P, Roux JJL. Urbanization and Carpobrotus edulis invasion alter the diversity and composition of soil bacterial communities in coastal areas. FEMS Microbiol Ecol 2020; 96:5848193. [PMID: 32463431 DOI: 10.1093/femsec/fiaa106] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 05/27/2020] [Indexed: 11/13/2022] Open
Abstract
Coastal dunes are ecosystems of high conservation value that are strongly impacted by human disturbances and biological invasions in many parts of the world. Here, we assessed how urbanization and Carpobrotus edulis invasion affect soil bacterial communities on the north-western coast of Spain, by comparing the diversity, structure and composition of soil bacterial communities in invaded and uninvaded soils from urban and natural coastal dune areas. Our results suggest that coastal dune bacterial communities contain large numbers of rare taxa, mainly belonging to the phyla Actinobacteria and Proteobacteria. We found that the presence of the invasive C. edulis increased the diversity of soil bacteria and changed community composition, while urbanization only influenced bacterial community composition. Furthermore, the effects of invasion on community composition were conditional on urbanization. These results were contrary to predictions, as both C. edulis invasion and urbanization have been shown to affect soil abiotic conditions of the studied coastal dunes in a similar manner, and therefore were expected to have similar effects on soil bacterial communities. Our results suggest that other factors (e.g. pollution) might be influencing the impact of urbanization on soil bacterial communities, preventing an increase in the diversity of soil bacteria in urban areas.
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Affiliation(s)
- Ana Novoa
- Department of Invasion Ecology, Institute of Botany, Czech Academy of Sciences, CZ-252 43 Průhonice, Czech Republic.,Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, 7602 Matieland, South Africa.,Invasive Species Programme, South African National Biodiversity Institute, Kirstenbosch Research Centre, 7735 Claremont, South Africa
| | - Jan-Hendrik Keet
- Department of Botany and Zoology, Stellenbosch University, 7602 Matieland, South Africa
| | - Yaiza Lechuga-Lago
- Laboratorio de investigación n21, Ecofisioloxía, Departamento de Bioloxía Vexetal e Ciencias do Solo, Edificio de Ciencias Experimentais, University of Vigo, Campus Universitario, As Lagoas Marcosende, 36310 Vigo, Pontevedra, Spain
| | - Petr Pyšek
- Department of Invasion Ecology, Institute of Botany, Czech Academy of Sciences, CZ-252 43 Průhonice, Czech Republic.,Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, 7602 Matieland, South Africa.,Department of Ecology, Faculty of Science, Charles University, Viničná 7, CZ-128 44 Prague, Czech Republic
| | - Johannes J Le Roux
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, 7602 Matieland, South Africa.,Department of Botany and Zoology, Stellenbosch University, 7602 Matieland, South Africa.,Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
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11
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Jurburg SD, Shek KL, McGuire K. Soil microbial composition varies in response to coffee agroecosystem management. FEMS Microbiol Ecol 2020; 96:5892097. [DOI: 10.1093/femsec/fiaa164] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/11/2020] [Indexed: 12/22/2022] Open
Abstract
ABSTRACT
Soil microbes are essential to the continued productivity of sustainably managed agroecosystems. In shade coffee plantations, the relationship between soil microbial composition, soil nutrient availability and coffee productivity have been demonstrated, but the effects of management on the composition of the soil microbial communities remains relatively unexplored. To further understand how management modulates the soil microbiome, the soil fungal and bacterial communities, soil chemistry, and canopy composition were surveyed in a Nicaraguan coffee cooperative, across 19 individual farms. Amplicon sequencing analyses showed that management (organic or conventional), stand age and previous land use affected the soil microbiome, albeit in different ways. Bacterial communities were most strongly associated with soil chemistry, while fungal communities were more strongly associated with the composition of the canopy and historical land use of the coffee plantation. Notably, both fungal and bacterial richness decreased with stand age. In addition to revealing the first in-depth characterization of the soil microbiome in coffee plantations in Nicaragua, these results highlight how fungal and bacterial communities are simultaneously modulated by long-term land use legacies (i.e. an agricultural plot's previous land use) and short-term press disturbance (i.e. farm age).
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Affiliation(s)
- Stephanie D Jurburg
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscherplatz 5E, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Johannisallee 21-23,Leipzig, Germany
- Department of Ecology, Evolution & Environmental Biology, Columbia University, 1190 Amsterdam Ave, New York, NY, USA
| | - Katherine L Shek
- Department of Biology, University of Oregon, 1025 University St., Eugene, OR, USA
| | - Krista McGuire
- Department of Biology, University of Oregon, 1025 University St., Eugene, OR, USA
- Smithsonian Tropical Research Institute, Apartado 0843–03092, Balboa, Ancón, Republic of Panama
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12
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Monteiro DA, Fonseca EDS, Rodrigues RDAR, da Silva JJN, da Silva EP, Balieiro FDC, Alves BJR, Rachid CTCDC. Structural and functional shifts of soil prokaryotic community due to Eucalyptus plantation and rotation phase. Sci Rep 2020; 10:9075. [PMID: 32493970 PMCID: PMC7270125 DOI: 10.1038/s41598-020-66004-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/27/2020] [Indexed: 11/09/2022] Open
Abstract
Agriculture, forestry and other land uses are currently the second highest source of anthropogenic greenhouse gases (GHGs) emissions. In soil, these gases derive from microbial activity, during carbon (C) and nitrogen (N) cycling. To investigate how Eucalyptus land use and growth period impact the microbial community, GHG fluxes and inorganic N levels, and if there is a link among these variables, we monitored three adjacent areas for 9 months: a recently planted Eucalyptus area, fully developed Eucalyptus forest (final of rotation) and native forest. We assessed the microbial community using 16S rRNA gene sequencing and qPCR of key genes involved in C and N cycles. No considerable differences in GHG flux were evident among the areas, but logging considerably increased inorganic N levels. Eucalyptus areas displayed richer and more diverse communities, with selection for specific groups. Land use influenced communities more extensively than the time of sampling or growth phase, although all were significant modulators. Several microbial groups and genes shifted temporally, and inorganic N levels shaped several of these changes. No correlations among microbial groups or genes and GHG were found, suggesting no link among these variables in this short-rotation Eucalyptus study.
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Affiliation(s)
- Douglas Alfradique Monteiro
- LABEM - Laboratory of Biotechnology and Microbial Ecology, Institute of Microbiology Paulo de Góes, Department of General Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eduardo da Silva Fonseca
- LABEM - Laboratory of Biotechnology and Microbial Ecology, Institute of Microbiology Paulo de Góes, Department of General Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | | | - Caio Tavora Coelho da Costa Rachid
- LABEM - Laboratory of Biotechnology and Microbial Ecology, Institute of Microbiology Paulo de Góes, Department of General Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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